Losing
by we will be 4ever and always
Summary: Two months after Emily drags in a new born baby into the TARDIS Madame Kovarian tries to kidnap both of them, leaving just The Doctor to save them. But can he save both of them?


The Doctor watched at Emily, who was six, walk into the TARDIS dragging with her something. Suddenly, he realized it was a tiny little baby in bright blue footsie pajamas, and he was about to cry as she carried him up the stairs. "Emily! What are you doing with that... that baby?!"

"I found in front of the Orpanage, what ever that is,"

"You mean the Orphanage?" asked The Doctor. Emily shrugged as she brought the baby all the way up the stairs. "Sweetie, we can't keep the baby. You have to put it back where you found..." he looked at the baby more closely. "him... I think,"

Emily stamped her foot as she dropped the baby's arms. He whimpered softly. "I already named him, daddy. I named him Sammy 'cause that's my favorite name for a boy!" Emily protested. The Doctor sighed and looked down at the baby. He picked him and that's when he started crying. "I don't think he likes you, daddy,"

The Doctor looked down at his daughter and rocked the baby in his arms. He quieted down as he sat on the couch. Emily walked over and sat next to him. "Can we please keep him, daddy? I promise I'll take of him the most," The Doctor laughed and kissed the top of her head. She smiled and leaned on him. "Is that a yes?"

"Alright. We can keep him," said The Doctor. Emily smiled and jumped off the couch. She started jumping up and down and smiled at her.

"Can I hold him, daddy?" she asked. He nodded as she sat down again. He handed him to her as she balanced him carefully in his arms and smiled down at him. "I think he likes me, daddy," she said. He smiled at her and wrapped an arm around her. Maybe this wasn't such a terrible idea.

* * *

The Doctor woke up by Samson crying in his crib. He sighed and got up and looked down at the crib and the two month old baby inside. He leaned down and picked him and rocked him in his arms. "Shh, it's OK buddy. Daddy's here now," he said as he cried. The Doctor bounced him in his arms as he yawned and sat down. That's when a tired looking Emily walked into the doorway and rubbed her eyes. She was wearing red footsie pajamas and clutching a little stuffed doll. She waddled in and walked up to her dad.

He looked over at her and smiled. "I can't sleep, daddy. Sammy's keeping me up," she walked closer and sat next to him. Emily rested her body on his shoulder and closed her eyes as Samson started to clam down. Suddenly, the TARDIS jolted forward and Samson began to cry again. The Doctor looked around frantically as Emily was sent to the floor. "Daddy!" she squealed.

"Calm down, Emily," he said. He stood and helped Emily up. "Will you watch Samson?" she nodded. "If he starts to cry just calm him down and only follow me if his asleep and is settled down. Alright?" The Doctor asked. Emily nodded as she was handed Samson. The Doctor walked out of the room and to the Control Room. Emily settled herself on the bed with the baby as he begun to sleep again. The TARDIS moved again, but he was already asleep. That's when Emily heard The Doctor yell and she stood up quickly.

Samson was asleep so she set him back in the crib and quietly walked out of the room. "No!" she heard him yell. "You can't have either of them!"

"Choose, Doctor. I know you have a new baby, so I'd choose him," Emily recognized the voice. It was Madame Kovarian. "Or Emily. She'll remember you giving her up," As she approached the Control Room she could see Silence's behind her and her dad being held back by two. "Tick tock, Doctor. Or I'll have to choose both of them." Emily peeked behind the wall and watched closely.

"You can have neither. Why are you so obsessed with my children?"

"Because it will cause you pain and guilt," That's when Madame Kovarian noticed Emily peeking behind the door. "Emily Song, why don't you come out?" she did but didn't move any closer. "This won't be a hard decision. Why don't you come closer dear?" she shook her head as Emily looked at her father. "Why don't you just give up, Doctor, or you'll loose both of them,"

The Doctor hung his head and mumbled, "I choose... Emily," Emily gasped but he quickly winked at her.

"Good choice. Now, say your goodbyes and she'll be coming with us," Emily ran down the stairs and to her dad. The Silence let go of him as he leaned down to her level. He whispered something to her and she nodded. They faked their goodbyes as she looked at Madame Kovarian. "Can I go grab something really quickly?"

She sighed but nodded her head as Emily ran up the steps. "Children. Always needing something," Kovarian remarked.

_Emily_

Emily ran into The Doctor's room and grabbed Samson then ran down the TARDIS corridors, remembering his words perfectly. _Grab Samson and run until you know your safe. _She ran faster as Samson stirred in her arms, preying he wouldn't wake up. Eventually he woke up, and being in new surrounding, started crying softly. "No, Samson, please. Were not safe yet. Daddy said to run until your safe. We aren't safe yet, please don't cry,"

That shut him up and he didn't cry. She kept running even though she was tired and wanted to stop. She did and leaned against a wall. She was out of breath and wanted her dad. She wished the Silence and Madame Kovarian would leave them alone. She wished her dad didn't have so many enemy's and they didn't have to run away from them.

Suddenly, she heard someone walking around so she quickly got up and ran. She ran faster than before, making sure no one caught her. But it was too late. A Silence stood in front of her and blocked her path. She held back a scream as it lifted her up and another took the baby out of her arms. Emily couldn't do anything so she let them control her as she began to cry. She failed her dad and would be separated from him.

_Doctor (and eventually everyone) _

Madame Kovarian smirked at The Doctor as she sent the Silence to capture his daughter and son. "I guess your planned failed, Doctor. Your daughter isn't that fast," He just scowled at her as she walked closer to him. "If you had just brought Emily to me you would still have your baby. But your too stubborn for that. You have to save everyone and beat everyone for your own good. Just let someone else win for once,"

The Doctor didn't say anything just stared at her. "The silent treatment now. Someone's angry," Madame Kovarian said. Right as she did they heard a scream and a tiny baby crying. The Doctor sighed, trying not to cry.

"Lemme go!" Emily yelled as they entered the room. A Silence was holding her and another was holding Samson as they walked to Madame Kovarian. "No!" she yelled. "Daddy!" he couldn't do anything to help her. They handed Emily to Madame Kovarian and she squirmed in her arms.

"Calm down, sweetie. You'll see your daddy eventually. Just not for awhile," she screamed and cried as Samson also cried. "Shut them up," she ordered the Silence. They put them to sleep as The Doctor watched everything, not saying a word. "Good bye, Doctor. Till we meet again," They all walked out of the TARDIS and the two Silence's that held him let go and walked off.

Just The Doctor was left now, his children gone and he was alone. With no one to help him. Just... Him.

_Emily and Samson (and eventually everyone) _

Emily and Samson both slept as they were brought to the same white room as before. "They won't need a cell just yet. At least the baby won't," said Madame Kovarian. They set both children on the ground and left them in the locked white room. After a couple hours Emily woke up.

"Daddy!" she screamed as she sat up and looked at her surroundings. She knew where she was and she didn't like it. Emily stood and walked over to the door. She knew it would be locked and she didn't have her Screwdriver with her so she couldn't do anything to help them. Samson stirred in his sleep and whimpered softly. Emily looked over at him. How could she sneak out with a baby who couldn't even crawl. Suddenly, the door opened and she backed away.

Madame Kovarian walked in and smiled at Emily. "Don't be a cheeky one, now," Emily stared at her and sat down next to her baby brother. "Do you want to be put in another cell?" Emily shook her head and put her face in her knees. She started crying.

"I just want my daddy," she mumbled. Kovarian scoffed. "You keep saying I'll see him eventually, but I want him now!" Emily yelled crying more. Kovarian looked down at the little girl and picked her up.

"You'll have to get used to wanting him now, because it's going to be a very long time from now," said Kovarian. Emily squirmed in her arms and squealed. "I have to put you in a cell now. I can't have you getting away, now,"

"Don't take me away from my baby brother!" Samson started crying and Kovarian walked out and handed Emily to one of the Silence. She was screaming and crying as she usually was. Kovarian walked back into the room to deal with the baby. As she cradled him he cried more and wouldn't seem to stop.

"Stop whining, will you," she said. He didn't stop but cried harder. Kovarian sighed and continued to rock the baby. A silence walked in. "Emily is in her cell. What will we do with the child?"

She sighed again. "I'll get him to shut up, don't worry. Now make sure Emily says put this time," he left her with the small baby and she slowly began to grow irritated from his crying. "What's wrong with you? Who are you crying for?"

"He's crying for me," someone said behind him.

"And how do you know?" Kovarian said while turning around. There was The Doctor, standing proud and tall. "Oh look you it is. What a surprise,"

"You shouldn't leave me alone with a time machine. I'm going to catch up to you eventually,"

She scoffed. "You seem pretty cocky. What makes you so sure you going to win?"

He shrugged. "Now, why don't I take care of my own son?" she was hesitant but handed him the baby. He settled down and he smiled. "See. All you need is a little love and compassion and he calms down. But now... I escape," he pulled out his Sonic Screwdriver and pointed it at something mechanical and it sparked up. He ran out of the room as Madame Kovarian yelled at him down the hall.

"Catch him!" she screeched.

The Doctor quickly ran, trying to find Emily's cell. Eventually he found it and used his Sonic to open it. When he ran in he locked it and Emily perked up. "Daddy! I knew it wouldn't be a long time before I saw you!"

He smiled and sat on the bed with her. "Alright, sweetie. We have to get out of here fast. How did you get out last time?" she pointed to the vent. "Do you think you can go through it again?" she shook her head.

"I fell through last time and hurt myself. 'Member?"

"This wasn't your best plan, Doctor. We have the keys. I own this place," said Kovarian through the doors.

The Doctor patted Emily's head and set Samson down. "I can't fit through there, so I want you to bring Samson with and unlock the door outside so we can get away."

"Why don't we just leave now,"

"They'll thinks what will do and alarms will go off. Just trust me on this, sweetie,"

Emily picked up Samson as The Doctor opens the vent. "Take this," he hands her his Sonic. "Be careful, and don't fall this time," Emily smiled as he helped her up and she crawled through the vent. Everything was going fine until she found the spot where she fell. She knew it would happen again so she went slowly. Suddenly, Samson fell but Emily grabbed onto his hand. They were falling so she let them but gripped onto Samson and fell on her back.

It didn't hurt to bad but she still held back tears. She stood quickly and heard the alarms go off. She ran away quickly and to her cell. She made it and opened the door. The Doctor ran out and picked her up. "Let's run, kiddo," he said. They ran out and noticed Kovarian was already on their trail.

Emily giggled as The Doctor sped up. "What's so funny?" he asked, breathless.

"I know your going to win," she said.

He smiled and continued to run. As he reached the room where the TARDIS was, he it suddenly locked and his Screwdriver flew from his hands. He turned around and was met with Madame Kovarian in front of them. Emily winced when she saw and held Samson closer. The Doctor set Emily down and she ran behind his legs. He walked closer as Emily stayed behind. "What now? Do you think I'm going to surrender and give them up, or our you just going to take them from me?"

"I guess I haven't decided yet, Doctor. But it's more likely your going to make the decision of running away, which will fail and leave you in the guilt of losing your children for the, what, second time?" said Madame Kovarian.

The Doctor laughed. "Give it a rest. Even my daughter knows that I'm going to win. You should take a lesson from her," The Doctor said. Kovarian smirked and looked back at them. Suddenly, Emily felt herself being drug toward them. The Doctor looked at her suspiciously, knowing she was the source when his daughter was right in front of her. Kovarian picked up the baby and rocked it slightly. She handed him to The Doctor, who took it and looked at her confused. "What are you doing?"

That's when she pulled out a gun and shot it at The Doctor, just missing him. He backed away as Kovarian took a handful of Emily's hair and pointed the gun at her. "You can either leave this place, kill you and the baby, or loose your daughter. Your choice, Doctor,"

He looked over at Emily, who was sobbing, and thought of. _Either way I lose at least one of them and Emily is stuck with Kovarian. _he thought. The Doctor sighed and walked over to pick up his Sonic Screwdriver. "Good choice, Doctor. Now, say goodbye to your daughter," Kovarian said as he walked back to Emily. She had let go of her hair so she was free. She ran over to her dad and hugged him and the baby tightly. She was still sobbing at The Doctor whispered on last thing in her ear. "I will see you again,"

The Doctor opened the door with the Screwdriver and walked into the room, closing the door behind him. The Doctor held back tears as he walked into the TARDIS and walked back into his room and set Samson in his crib. He was still sound asleep as before as he sat at the edge of the bed and covered his eyes and begun to cry. He didn't know how long it would be before he saw her again. He couldn't riskl losing Samson so he decided to fly away, and not look back.

_Emily _

Emily watched as her father walked away from her and Madame Kovarian walked up behind her. She picked her up and walked away. Emily was still sobbing and started kicking and hitting her as she brought her back to her cell. "Lemme go! Please!" she begged as she was tossed into her cell. She balled herself up on the bed and continued to cry.

**I know this all so depressing but I'm bored and don't know what else should write. And also, I'm so sorry in my other Doctor Who fanfic I haven't updated for a while but I just have, like, lost all inspiration for it, so I'll try to update more in it as soon as I can. Sorry! :P Hope you liked this story and... yeah... **


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